Would the output be affected much if I used EPUB as an intermediary conversion format in between different ebook formats (e.g. Amazon Kindle's AZW3/MOBI) and PDF?

While it may seem an odd idea at first glance, my reasoning is quite simple: I want to minimize the number of ebook formats in my collection, but I don't want to mess with their layout. Automatic "unsupervised" conversion of a large number of books in my rather limited experience only works well between formats that have the same basic type of layout. Therefore, I want to convert all scroll/browsing-based formats (e.g. AZW, MOBI) to EPUB and all page-based formats (e.g. DJVU) to PDF.

At a later stage, I may find the time and motivation to manually convert all or some of these EPUB books to PDF and inspect/readjust the way the margins and page-breaks are organized.

In most instances, such as when reencoding audio or video, adding an additional conversion step would be a huge no no because of the loss in quality, but with ebooks I feel that the situation is somewhat different.

I would assume that any change in page layout during the conversion between, say, MOBI and EPUB is so miniscule compared to the changes that occur in the page layout with the conversion between EPUB and PDF, that there shouldn't be much concern over the use of EPUB as an intermediary format?

In other words, I may leave all these converted files as EPUB indefinitely in which case it's a simple one-step conversion without intermediary formats and thus no potential problems due to multiple conversion steps will arise. Or, I might convert them to PDF later on but in that case the very conversion to PDF (from scroll-based to page-based content layout) will change the layout so much that the fact that the book was already converted to EPUB won't make any real observable difference.